plot_mir_count_threshold: Plot occurrence count of miRNA names over different...
In JulFriedrich/miRetrieve: miRNA Text Mining in Abstracts

Description Usage Arguments Details Value See Also

Plot occurrence count of distinct miRNA names over different thresholds.

plot_mir_count_threshold(
  df,
  start = 1,
  end = 5,
  bins = NULL,
  colour = "steelblue3",
  col.mir = miRNA,
  col.pmid = PMID,
  title = NULL
)

`df`	Data frame containing columns with miRNAs and PubMed-IDs.
`start`	Integer or float. Must be greater than 0 and smaller than `end`.
`end`	Integer or float. Must be greater than 0 and greater than `start`. If `start` >= 1, `plot_mir_count_threshold()` plots number of miRNAs above different absolute thresholds, ranging from `start` to `end`. If `start` >= 0 and `end` <= 1, `bins` must be specified. If `bins` is not specified, `bins` is automatically set to `10`. `plot_mir_count_threshold()` then plots number of miRNAs above different thresholds, ranging from `start` to `end` in n `bins`. If `start` >= 0 and `end` <= 1 and the value of `start` is too low for the number of miRNAs to be plotted, `plot_mir_count_threshold()` raises a warning, suggesting a more appropriate `start` value.
`bins`	Integer. Optional. Only necessary if `start` >=0 and `end` <=1. Specifies number of bins between `start` and `end`. If `start` >= 0, `end` <= 1, and `bins` is not specified, `bins` is automatically set to `10`.
`colour`	String. Colour of bar plot.
`col.mir`	Symbol. Column containing miRNAs.
`col.pmid`	Symbol. Column containing PubMed-IDs.
`title`	String. Plot title.

Plot occurrence of distinct miRNA names over different thresholds. These thresholds can either be absolute values or floating values between 0 and 1. If the thresholds are absolute values, number of distinct miRNA names mentioned in at least n abstracts are plotted, where n is the range of thresholds defined by start and end. If the thresholds are floating values, bins must be specified as well. Then the umber of distinct miRNA names mentioned in at least n abstracts over bins are plotted, where n is the range of thresholds between start and end. Overall, plotting can help in identifying if the abstracts at hand mention different miRNAs in a balanced way, or if there are few miRNAs dominating the field.

Bar plot counting the occurrence of miRNA names above different thresholds.

count_mir_threshold(), count_mir(), plot_mir_count()

Other count functions: count_mir_threshold(), count_mir(), count_snp(), plot_mir_count()

JulFriedrich/miRetrieve documentation built on Sept. 20, 2021, 11:37 p.m.